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- PDB-6xv4: Neutron structure of ferric ascorbate peroxidase-ascorbate complex -

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Basic information

Entry
Database: PDB / ID: 6xv4
TitleNeutron structure of ferric ascorbate peroxidase-ascorbate complex
ComponentsAscorbate peroxidase
KeywordsOXIDOREDUCTASE / ascorbate peroxidase / neutron crystallography / heme peroxidase / proton pathway
Function / homology
Function and homology information


L-ascorbate peroxidase / L-ascorbate peroxidase activity / cellular response to oxidative stress / heme binding / metal ion binding
Similarity search - Function
Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily
Similarity search - Domain/homology
ASCORBIC ACID / DEUTERATED WATER / PROTOPORPHYRIN IX CONTAINING FE / : / L-ascorbate peroxidase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKwon, H. / Basran, J. / Devos, J.M. / Schrader, T.E. / Ostermann, A. / Blakeley, M.P. / Raven, E.L. / Moody, P.C.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N015940/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Visualizing the protons in a metalloenzyme electron proton transfer pathway.
Authors: Kwon, H. / Basran, J. / Devos, J.M. / Suardiaz, R. / van der Kamp, M.W. / Mulholland, A.J. / Schrader, T.E. / Ostermann, A. / Blakeley, M.P. / Moody, P.C.E. / Raven, E.L.
History
DepositionJan 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3866
Polymers28,3621
Non-polymers1,0245
Water6,557364
1
A: Ascorbate peroxidase
hetero molecules

A: Ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,77112
Polymers56,7242
Non-polymers2,04810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_735y+2,x-2,-z1
Buried area4280 Å2
ΔGint-96 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.862, 81.862, 74.969
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-421-

DOD

21A-436-

DOD

31A-607-

DOD

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Ascorbate peroxidase / / Cytosolic ascorbate peroxidase 1 / Uncharacterized protein


Mass: 28361.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: apx1, GLYMA_U021900 / Production host: Escherichia coli (E. coli) / References: UniProt: Q43758, L-ascorbate peroxidase
#5: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM

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Non-polymers , 4 types, 368 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: D2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: Lithium sulfate HEPES

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORFRM II BIODIFF13.4
ROTATING ANODERIGAKU MICROMAX-007 HF21.54
Detector
TypeIDDetectorDate
BIODIFF1IMAGE PLATEFeb 1, 2017
RIGAKU SATURN 9442CCDMar 1, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
13.41
21.541
Reflection

Entry-ID: 6XV4 / Rmerge(I) obs: 0.2

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Diffraction-IDNet I/σ(I)
2.1-36.21436891.1313.9
1.9-20.420067899.910.926.9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsDiffraction-ID
2.1-2.160.410341
1.9-1.940.613692

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
Refinement

% reflection Rfree: 10 % / SU ML: 0.16 / Cross valid method: THROUGHOUT / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 18.98 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 5JPR

5jpr

Resolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection obs (%)σ(F)
1.9-20.47X-RAY DIFFRACTION96.9821.62591.160.22580.16510.171220652064299.981.35
2.09-35.93NEUTRON DIFFRACTION0.29830.210.218714351434891.250
Refinement stepCycle: final / Resolution: 1.9→20.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1899 0 103 1046 3048
Biso mean--19.91 33.01 -
Num. residues----248
LS refinement shell

Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.160.34591240.24251115NEUTRON DIFFRACTION81
2.16-2.250.31021270.22881146NEUTRON DIFFRACTION83
2.25-2.350.32421330.21961193NEUTRON DIFFRACTION85
2.35-2.470.2921370.21931238NEUTRON DIFFRACTION89
2.47-2.630.3081410.22021259NEUTRON DIFFRACTION91
2.63-2.830.30431390.21651261NEUTRON DIFFRACTION90
2.83-3.120.30561490.22231336NEUTRON DIFFRACTION95
3.12-3.560.29221550.19091396NEUTRON DIFFRACTION98
3.57-4.490.25191600.16261438NEUTRON DIFFRACTION99
1.9-1.940.22291360.18981221X-RAY DIFFRACTION100
1.94-1.990.21811340.1771201X-RAY DIFFRACTION100
1.99-2.050.22761340.1651213X-RAY DIFFRACTION100
2.05-2.110.23151360.15551222X-RAY DIFFRACTION100
2.11-2.170.22061350.15531216X-RAY DIFFRACTION100
2.17-2.250.22971350.17151219X-RAY DIFFRACTION100
2.25-2.340.2361370.15551227X-RAY DIFFRACTION100
2.34-2.450.2331340.1531213X-RAY DIFFRACTION100
2.45-2.580.22241390.15311234X-RAY DIFFRACTION100
2.58-2.740.2311350.16731226X-RAY DIFFRACTION100
2.74-2.950.24621380.1681240X-RAY DIFFRACTION100
2.95-3.250.24381370.17541249X-RAY DIFFRACTION100
3.25-3.710.20841410.15251261X-RAY DIFFRACTION100
3.71-4.670.19011410.15151277X-RAY DIFFRACTION100

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